PedCrossSel function #9
Description
We want a stable version of pedigreeCross() able to show patterns of selection.
Using a founder population and a set pedigree, pedigreeCross() creates a pop object by spreading the haplotypes (via makeCross2) following the pedigree.
If selection is applied, individual ID can be swapped to respect selection principles while keeping the same pedigree structure.
Individuals are ranked within each generation and sex based on the chosen criteria, and based on their number of offspring. A mismatch of those two rankings provokes a rewriting of the ID. The creation of the genomes with makeCross2 is then done with the new pedigree information.
This part has been implemented when selecting with 'gv' values for any traits in SP. Providing information on sex is necessary for the moment.
TO DO:
Selection on 'ebv', 'pheno' and 'function'. Genetic values are automatically set with makeCross2 but not the rest. A step needs to be added to add those values when individuals are created, to be able to select the individuals using them in the next generation.
matchID option is not working at the moment. See issue #7 (comment)
DH and selfing has been deprecated compared to pedigreeCross. A common ranking could allow for ID rewriting and selfing.
Pedigree that has not been recoded as 1:n individuals will likely break the function or give incorrect results. More testings are necessary after fixing #6 (comment)